It's somewhat a moot point though, because everyone likes to gzip their nifti and unfortunately the file formats don't have a uniformly-accepted way to leverage the huge disk savings we can get from masked data without applying (stupid from the point of view of the types of analysis we do) compression. Even filesystem-level compression doesn't help. If you can fit all your data into available RAM, you're fine. If not...
http://www.mathworks.com/help/matlab/memory-mapping.html
It's somewhat a moot point though, because everyone likes to gzip their nifti and unfortunately the file formats don't have a uniformly-accepted way to leverage the huge disk savings we can get from masked data without applying (stupid from the point of view of the types of analysis we do) compression. Even filesystem-level compression doesn't help. If you can fit all your data into available RAM, you're fine. If not...